Fig. 1
From: Molecular and Evolutionary Analysis of the Hd6 Photoperiod Sensitivity Gene Within Genus Oryza
Analysis of sequence similarity within the Hd6 region of the studied species. a Conservation plot for nucleotides of the 20 cultivated varieties and wild rice species. The vertical axis represents the proportion (percent) of conserved nucleotides at each site (i.e., the proportion that are identical to the consensus sequence), and the values were calculated using a window size of 100 bp with a sliding 10-bp interval. In the diagram of Hd6 above the plot, the black boxes represent exons 1 to 10 from the 5′ (left) to the 3′ (right) end. b Distribution of SNPs between species (vertical white bars) detected within the coding region of Hd6 (using Kasalath as the reference sequence). Arrows indicate nonsynonymous substitution sites. Boxes above the graph represent conserved subdomains of CK2α numbered I to XI from the 5′ (left) to the 3′ (right) end of its nucleotide sequence. 1 O. sativa cv. Kasalath, 2 O. sativa cv. Shuusoushu, 3 O. sativa cv. 93–11, 4 O. sativa cv. Nipponbare, 5 O. sativa cv. Khau Mac Kho, 6 O. rufipogon W0106, 7 O. rufipogon W0574, 8 O. rufipogon W1943, 9 O. glaberrima, 10 O. barthii, 11 O. glumaepatula, 12 O. meridionalis, 13 O. longistaminata, 14 O. punctata, 15 O. minuta (OM_Ba0079N19), 16 O. minuta (OM_Ba0144F13), 17 O. officinalis, 18 O. alta, 19 O. australiensis, 20 O. brachyantha, 21 O. granulata.